So this is where I am at so far.
new batteries
new alternator
new GPR

here is the backstory:
just about 2 weeks back from now, I was driving home from campus and that id10T light (red battery icon) came on and the scangaugeii showed the voltage drop from the usual 13-14+VDC to just 12.5VDC … and that slowly trickled down to 11.9VDC when I got home.

it sat for a day or so. 1st step I called about warranty status on batteries & if they had a space for me to quickly drive down to test the batteries. I was in luck and when I arrived they tested them. [edit to speed up ]
Batteries were under warranty and had been swapped; all those wires and terminals cleaned at that time. Discovered the voltage didn’t return to normal when started truck at that shop. So I called and talked with CSR on looking up my history for the alternator warranty possibly… “Yup, come on over, you have it. A lifetime warranty and that one is 11 years old. So we swapped it out twice. Might have been bad out of the box. The managers call not mine.
we looked up on web some things and then I went home to open up FTE and search for anything…

well, searched back n forth over the last week. Read over 20 threads. Nothing really helped - conclusively… so on a whim I tested the terminals on the GPR and the 2 small terminals gave iffy contact and wierd resistance levels.
so replaced it while also unwrapping the main wire loom that the BK/OG big wire was suspended in along the lip of the firewall… that was a mess!
Next, tested resistance on both of those wires to see what the fusible links did… both batches of fusible links seemed to pass with resistance showing quickly. Can not test each solo without cutting and removing them.

I cleaned each of these BK/OG terminals before testing. I have reassembled everything.
I had chased All wires to show good data at this point. I guess what left is to use the graph of voltage levels that are in one of the threads I still have open on the desktop inside….
meanwhile I eventually also Swapped the GPR (Glow Plug Relay) because it had a wierd reaction to multimeter.

so here is the link to the YouTube video I just uploaded to show:
a) how quick it starts when “cold”
b) view of dash & scangaugeii to show real time voltage validating that the alternator will not turn on….

i have run it for over 5 minutes before this video was created here and now - today…..

not sure what else I can do to test, trouble shoot or what words to use to solve this mystery of no charging now. I am aware of a few comments in a couple threads talk about the possible “PCM” failure?

well, here’s the YouTube link {edit to try this supposedly correct link}:
dang it…. I will come back from desktop as it did not let me share it as I wrote this originally from iPhone across from YouTube app.

here’s a few pics to reference everything done so far…

The new alternator… you can almost see the oem GPR?

The new GPR.

The oem solenoid and fusible links still showing as working.

Full engine bay… relax, batteries had been relocated… to next picture.

Passenger side frame rail location under bed.

 

Have you checked for battery voltage on the charge post of the alternator and switched ignition voltage at the pigtail?
Continuity between the battery negative post and the alternator case?

 

Check your main cables for swelling. Corrosion under the insulation can also cause a lot of resistance. I have had to replace a few cable ends for an issue like yours on different vehicles and my truck.
Also on the solenoid I had to once clean all terminals and wire ends for proper contact.
Even missed connecting a wire to the solenoid and tried blaming a bad alternator.. at first.

 

You said you've replaced the glow plug relay? Have you done any checking w/ a volt meter to make sure it's turning off - or disabled it altogether to make sure it's not still running?

 

yes to both parts of 1st question.
i will gladly test the 2nd question very soon...

I have been very proactive about the cables ever since i converted the battery cables to the rear location. Usually 1 to 3 times a year i will clean the battery tray, and wire brush clean all the terminals and the grounding points and wires.

swapped the GPR, yes. BUT... I will definately try this test when I get time to do the test referenced above....

From 2003 FSM (factory service manual but not the wiring diagram manual) [edited to add the model year of manual]
regarding what i got accomplished today....
From the CJB (Central Junction Box) next to the brake booster
**There is no Fuse port 45 - that is even in the box
all fuses were good
especially Fuse #12 - 20A
VDC @ B+ = to battery (+) = 12.05V (KOEO engine off)



from 2003* FSM section 414-00-5 Pinpoint test(s) B
disconnect BK/OG at ALT to GPR = (ohm resistance), yes
"/ " GPR to Starter solenoid = (Nope) on pass terminal & ((yes)) on drivers side terminal
KOEO engine running
curcuit 36 (B+) to ground = 12.2V (once started and up to over 3 minutes running (i even rev'ed up to 1700+ for a sustained while))
port 904 (in disconnected pigtail) v= 0.25V
port 904 (in alternator) v=1.52V
port 35 (in disconnected pigtail) v=11.94V
port 35 (in alternator) v= 0.00V

KOEO(?) engine off
port 904 (in disconnected pigtail) v= 0.5V
port 904 (in alternator) v=1.52V
port 35 (in disconnected pigtail) v=12.04V
port 35 (in alternator) v= 0.03V

my friend who owns an autoshop let me hop on his work PC's special website account for shops nationwide to use and something popped up that i took note of... the LG/RD wires from the plug "C185" on the back of the alternator that can ground out that will keep the "icon on the dash" of a red battery lit even after replacing Alt and batteries etc.

so i started to unwrap and slightly separate those 2 LG/RD (light green/red stripe) wires that run to the multi-pin connector in top of the drivers valve cover...

get to track them back through the dash to test resistance for each as best i can to see where the likely "grounding out" is occuring.

Soooo, THAT is my current hunch right now as i wind down for bed.....

 

you can Fix the corrosion issue once and for all, with FLUID FILM.

Here are my batteries after two years ....
no corrosion at all, just dust that the non-drying stuff likes to collect.


Passenger side, I give them a fresh shot of Fluid Film every year....



the 'broken wire' was fixed 2 years ago, it goes to a #6 THHN pair of wires for the 12v Refrigerator in the back of the truck.

Spray everything that wants to rust with Fluid Film, that will be the last time you have to "clean it up"

 

Your low voltage of 12.2 volts with the engine at 1700 RPM plus the voltages going from 13-14 volts to ~12 volts all of a sudden, and then the battery voltage decreasing when driven more all point to the alternator either being bad or not turning on. The 1999 shop manual for the diesel engine single alternator starts at 414-00-26 and the pinpoint tests start with BA. The page numbers and pinpoint test letters you gave are for the gas engines which use the 3G alternator while the diesels use a 6G. You will want to perform pinpoint test BA on page 414-00-29 as that's the correct pinpoint test for your truck and problem.

 

sorry, my dyslexic/ADHD brain missed a key detail (in review before i clicked send) in my post that this reply of yours wasn't aware of because of my typo.
i just fixed that error. Your FSM is from 1999 and the manual i have is the 2003.
Sooooo, page 26 isn't the same for what i see. However, i shall be triple checking the specifics you speak of.